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Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: datp-udp complex
Analyse Structural mechanism of allosteric substrate specificity in a ribonucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XJG
- Type
- protein
- Length
- 1,225 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase, B12-dependent
- EC
- 1.17.4.1
- UniProt
- O33839
- Ligands
- UDP, DTP, MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 615 | 44% helix, 13% strand | O33839 |
| B | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 610 | 46% helix, 12% strand | O33839 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.74 | 0.79 | 79 | UDP, DTP |
| 2 | 617 | 0.71 | 0.79 | 77 | empty |
| 3 | 581 | 0.68 | 0.78 | 55 | UDP |
| 4 | 487 | 0.66 | 0.78 | 68 | empty |
| 5 | 100 | 0.63 | 0.88 | 19 | DTP |
Interfaces
1 interface between chains.
- A–B · 1179 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1XJG · Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O33839
- Elsewhere: RCSB PDB 1XJG · PDBe 1XJG · UniProt O33839
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